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- EMDB-14312: phospho-STING binding to adaptor protein complex-1 -

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Basic information

Entry
Database: EMDB / ID: EMD-14312
Titlephospho-STING binding to adaptor protein complex-1
Map data
Sample
  • Complex: phospho-STING binding to adaptor protein complex-1
    • Protein or peptide: AP-1 complex subunit beta-1
    • Protein or peptide: ADP-ribosylation factor 1
    • Protein or peptide: AP-1 complex subunit gamma-1
    • Protein or peptide: Stimulator of interferon genes protein
    • Protein or peptide: AP-1 complex subunit mu-1
    • Protein or peptide: AP-1 complex subunit sigma-3
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
Function / homology
Function and homology information


basolateral protein secretion / mitotic cleavage furrow ingression / endosome to melanosome transport / trans-Golgi Network Vesicle Budding / AP-1 adaptor complex / Lysosome Vesicle Biogenesis / platelet dense granule organization / Glycosphingolipid transport / regulation of receptor internalization / melanosome assembly ...basolateral protein secretion / mitotic cleavage furrow ingression / endosome to melanosome transport / trans-Golgi Network Vesicle Budding / AP-1 adaptor complex / Lysosome Vesicle Biogenesis / platelet dense granule organization / Glycosphingolipid transport / regulation of receptor internalization / melanosome assembly / STING complex / Intra-Golgi traffic / STING mediated induction of host immune responses / regulation of Arp2/3 complex-mediated actin nucleation / Golgi to vacuole transport / STAT6-mediated induction of chemokines / Synthesis of PIPs at the Golgi membrane / Golgi Associated Vesicle Biogenesis / serine/threonine protein kinase complex / protein localization to endoplasmic reticulum / 2',3'-cyclic GMP-AMP binding / clathrin adaptor activity / proton channel activity / cyclic-di-GMP binding / pattern recognition receptor signaling pathway / cGAS/STING signaling pathway / IRF3-mediated induction of type I IFN / MHC class II antigen presentation / Nef Mediated CD4 Down-regulation / dendritic spine organization / positive regulation of type I interferon-mediated signaling pathway / cytoplasmic pattern recognition receptor signaling pathway / determination of left/right symmetry / long-term synaptic depression / reticulophagy / clathrin-coated vesicle / COPI-dependent Golgi-to-ER retrograde traffic / cellular response to exogenous dsRNA / Lysosome Vesicle Biogenesis / clathrin binding / Golgi Associated Vesicle Biogenesis / cell leading edge / Synthesis of PIPs at the plasma membrane / cellular response to organic cyclic compound / positive regulation of type I interferon production / positive regulation of macroautophagy / protein complex oligomerization / autophagosome membrane / autophagosome assembly / intracellular copper ion homeostasis / protein targeting / cellular response to interferon-beta / positive regulation of defense response to virus by host / COPI-mediated anterograde transport / signaling adaptor activity / activation of innate immune response / clathrin-coated pit / antiviral innate immune response / vesicle-mediated transport / endoplasmic reticulum-Golgi intermediate compartment membrane / MHC class II antigen presentation / positive regulation of interferon-beta production / autophagosome / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / Regulation of innate immune responses to cytosolic DNA / Neutrophil degranulation / sarcomere / secretory granule membrane / small monomeric GTPase / kidney development / trans-Golgi network membrane / Nef mediated downregulation of MHC class I complex cell surface expression / intracellular protein transport / positive regulation of DNA-binding transcription factor activity / trans-Golgi network / cytoplasmic vesicle membrane / cellular response to virus / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of protein binding / peroxisome / heart development / presynapse / regulation of inflammatory response / defense response to virus / RNA polymerase II-specific DNA-binding transcription factor binding / mitochondrial outer membrane / postsynaptic density / early endosome / endosome / neuron projection / protein domain specific binding / lysosomal membrane / Golgi membrane / intracellular membrane-bounded organelle / innate immune response / focal adhesion / GTPase activity / ubiquitin protein ligase binding / Neutrophil degranulation / synapse
Similarity search - Function
AP-1 complex subunit sigma / Adaptor protein complex AP-1, gamma subunit / Gamma-adaptin ear (GAE) domain / Gamma-adaptin ear (GAE) domain profile. / Adaptor protein complex, sigma subunit / ADP-ribosylation factor 1-5 / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / Beta-adaptin appendage, C-terminal subdomain / AP-1/2/4 complex subunit beta / Beta2-adaptin appendage, C-terminal sub-domain ...AP-1 complex subunit sigma / Adaptor protein complex AP-1, gamma subunit / Gamma-adaptin ear (GAE) domain / Gamma-adaptin ear (GAE) domain profile. / Adaptor protein complex, sigma subunit / ADP-ribosylation factor 1-5 / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / Beta-adaptin appendage, C-terminal subdomain / AP-1/2/4 complex subunit beta / Beta2-adaptin appendage, C-terminal sub-domain / Beta2-adaptin appendage, C-terminal sub-domain / AP complex subunit beta / : / Clathrin adaptor complex, small chain / Clathrin adaptor complexes small chain signature. / Clathrin adaptor complexes medium chain signature 1. / Clathrin adaptor, mu subunit / Clathrin adaptor, mu subunit, conserved site / Clathrin adaptor complexes medium chain signature 2. / : / Coatomer/calthrin adaptor appendage, C-terminal subdomain / : / Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily / Transmembrane protein 173 / Adaptor complexes medium subunit family / AP complex, mu/sigma subunit / Clathrin adaptor complex small chain / AP-2 complex subunit mu, C-terminal superfamily / Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain / Mu homology domain / Adaptin C-terminal domain / Mu homology domain (MHD) profile. / Adaptin C-terminal domain / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Adaptin N terminal region / Small GTPase superfamily, ARF type / Clathrin adaptor, appendage, Ig-like subdomain superfamily / small GTPase Arf family profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / Longin-like domain superfamily / ARF-like small GTPases; ARF, ADP-ribosylation factor / TBP domain superfamily / Armadillo/beta-catenin-like repeats / Armadillo / Rab subfamily of small GTPases / Armadillo-like helical / Small GTP-binding protein domain / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
AP-1 complex subunit gamma-1 / AP-1 complex subunit mu-1 / ADP-ribosylation factor 1 / AP-1 complex subunit beta-1 / Stimulator of interferon genes protein / AP-1 complex subunit sigma-3
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.34 Å
AuthorsXu P / Ablasser A
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)ALTF-184European Union
CitationJournal: Nature / Year: 2022
Title: Clathrin-associated AP-1 controls termination of STING signalling.
Authors: Ying Liu / Pengbiao Xu / Sophie Rivara / Chong Liu / Jonathan Ricci / Xuefeng Ren / James H Hurley / Andrea Ablasser /
Abstract: Stimulator of interferon genes (STING) functions downstream of cyclic GMP-AMP synthase in DNA sensing or as a direct receptor for bacterial cyclic dinucleotides and small molecules to activate ...Stimulator of interferon genes (STING) functions downstream of cyclic GMP-AMP synthase in DNA sensing or as a direct receptor for bacterial cyclic dinucleotides and small molecules to activate immunity during infection, cancer and immunotherapy. Precise regulation of STING is essential to ensure balanced immune responses and prevent detrimental autoinflammation. After activation, STING, a transmembrane protein, traffics from the endoplasmic reticulum to the Golgi, where its phosphorylation by the protein kinase TBK1 enables signal transduction. The mechanism that ends STING signalling at the Golgi remains unknown. Here we show that adaptor protein complex 1 (AP-1) controls the termination of STING-dependent immune activation. We find that AP-1 sorts phosphorylated STING into clathrin-coated transport vesicles for delivery to the endolysosomal system, where STING is degraded. We identify a highly conserved dileucine motif in the cytosolic C-terminal tail (CTT) of STING that, together with TBK1-dependent CTT phosphorylation, dictates the AP-1 engagement of STING. A cryo-electron microscopy structure of AP-1 in complex with phosphorylated STING explains the enhanced recognition of TBK1-activated STING. We show that suppression of AP-1 exacerbates STING-induced immune responses. Our results reveal a structural mechanism of negative regulation of STING and establish that the initiation of signalling is inextricably associated with its termination to enable transient activation of immunity.
History
DepositionFeb 8, 2022-
Header (metadata) releaseSep 14, 2022-
Map releaseSep 14, 2022-
UpdateNov 9, 2022-
Current statusNov 9, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14312.png

Downloads & links

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Map

FileDownload / File: emd_14312.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.9 Å/pix.
x 300 pix.
= 270. Å		0.9 Å/pix.
x 300 pix.
= 270. Å		0.9 Å/pix.
x 300 pix.
= 270. Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.055
Minimum - Maximum-0.18775003 - 0.4890242
Average (Standard dev.)0.0012783447 (±0.013376495)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 270.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_14312_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_14312_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : phospho-STING binding to adaptor protein complex-1

EntireName: phospho-STING binding to adaptor protein complex-1
Components
  • Complex: phospho-STING binding to adaptor protein complex-1
    • Protein or peptide: AP-1 complex subunit beta-1
    • Protein or peptide: ADP-ribosylation factor 1
    • Protein or peptide: AP-1 complex subunit gamma-1
    • Protein or peptide: Stimulator of interferon genes protein
    • Protein or peptide: AP-1 complex subunit mu-1
    • Protein or peptide: AP-1 complex subunit sigma-3
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: phospho-STING binding to adaptor protein complex-1

SupramoleculeName: phospho-STING binding to adaptor protein complex-1 / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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Macromolecule #1: AP-1 complex subunit beta-1

MacromoleculeName: AP-1 complex subunit beta-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 66.008422 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTDSKYFTTT KKGEIFELKA ELNSDKKEKK KEAVKKVIAS MTVGKDVSAL FPDVVNCMQT DNLELKKLVY LYLMNYAKSQ PDMAIMAVN TFVKDCEDPN PLIRALAVRT MGCIRVDKIT EYLCEPLRKC LKDEDPYVRK TAAVCVAKLH DINAQLVEDQ G FLDTLKDL ...String:
MTDSKYFTTT KKGEIFELKA ELNSDKKEKK KEAVKKVIAS MTVGKDVSAL FPDVVNCMQT DNLELKKLVY LYLMNYAKSQ PDMAIMAVN TFVKDCEDPN PLIRALAVRT MGCIRVDKIT EYLCEPLRKC LKDEDPYVRK TAAVCVAKLH DINAQLVEDQ G FLDTLKDL ISDSNPMVVA NAVAALSEIA ESHPSSNLLD LNPQSINKLL TALNECTEWG QIFILDCLAN YMPKDDREAQ SI CERVTPR LSHANSAVVL SAVKVLMKFM EMLSKDLDYY GTLLKKLAPP LVTLLSAEPE LQYVALRNIN LIVQKRPEIL KHE MKVFFV KYNDPIYVKL EKLDIMIRLA SQANIAQVLA ELREYATEVD VDFVRKAVRA IGRCAIKVEQ SAERCVSTLL DLIQ TKVNY VVQEAIVVIK DIFRKYPNKY ESVIATLCEN LDSLDEPEAR AAMIWIVGEY AERIDNADEL LESFLEGFHD KSTQV QLQL LTAIVKLFLK KPTETQELVQ QVLSLATQDS DNPDLRDRGY IYWRLLSTDP VAAKEVVLAE KPLISEETDL IEPTLL DEL ICYIGTLASV YHKPPSAFVE G

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Macromolecule #2: ADP-ribosylation factor 1

MacromoleculeName: ADP-ribosylation factor 1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.9366 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
EMRILMVGLD AAGKTTILYK LKLGEIVTTI PTIGFNVETV EYKNISFTVW DVGGLDKIRP LWRHYFQNTQ GLIFVVDSND RERVNEARE ELMRMLAEDE LRDAVLLVFA NKQDLPNAMN AAEITDKLGL HSLRHRNWYI QATCATSGDG LYEGLDWLSN Q LRNQK

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Macromolecule #3: AP-1 complex subunit gamma-1

MacromoleculeName: AP-1 complex subunit gamma-1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 67.399242 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MPAPIRLREL IRTIRTARTQ AEEREMIQKE CAAIRSSFRE EDNTYRCRNV AKLLYMHMLG YPAHFGQLEC LKLIASQKFT DKRIGYLGA MLLLDERQDV HLLMTNCIKN DLNHSTQFVQ GLALCTLGCM GSSEMCRDLA GEVEKLLKTS NSYLRKKAAL C AVHVIRKV ...String:
MPAPIRLREL IRTIRTARTQ AEEREMIQKE CAAIRSSFRE EDNTYRCRNV AKLLYMHMLG YPAHFGQLEC LKLIASQKFT DKRIGYLGA MLLLDERQDV HLLMTNCIKN DLNHSTQFVQ GLALCTLGCM GSSEMCRDLA GEVEKLLKTS NSYLRKKAAL C AVHVIRKV PELMEMFLPA TKNLLNEKNH GVLHTSVVLL TEMCERSPDM LAHFRKLVPQ LVRILKNLIM SGYSPEHDVS GI SDPFLQV RILRLLRILG RNDDDSSEAM NDILAQVATN TETSKNVGNA ILYETVLTIM DIKSESGLRV LAINILGRFL LNN DKNIRY VALTSLLKTV QTDHNAVQRH RSTIVDCLKD LDVSIKRRAM ELSFALVNGN NIRGMMKELL YFLDSCEPEF KADC ASGIF LAAEKYAPSK RWHIDTIMRV LTTAGSYVRD DAVPNLIQLI TNSVEMHAYT VQRLYKAILG DYSQQPLVQV AAWCI GEYG DLLVSGQCEE EEPIQVTEDE VLDILESVLI SNMSTSVTRG YALTAIMKLS TRFTCTVNRI KKVVSIYGSS IDVELQ QRA VEYNALFKKY DHMRSALLER MPVMEKVTTN GP

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Macromolecule #4: Stimulator of interferon genes protein

MacromoleculeName: Stimulator of interferon genes protein / type: protein_or_peptide / ID: 4 / Details: phospho-STING tail / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.065068 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
QEPELLI(SEP)G

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Macromolecule #5: AP-1 complex subunit mu-1

MacromoleculeName: AP-1 complex subunit mu-1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 48.60673 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSASAVYVLD LKGKVLICRN YRGDVDMSEV EHFMPILMEK EEEGMLSPIL AHGGVRFMWI KHNNLYLVAT SKKNACVSLV FSFLYKVVQ VFSEYFKELE EESIRDNFVI IYELLDELMD FGYPQTTDSK ILQEYITQEG HKLETGAPRP PATVTNAVSW R SEGIKYRK ...String:
MSASAVYVLD LKGKVLICRN YRGDVDMSEV EHFMPILMEK EEEGMLSPIL AHGGVRFMWI KHNNLYLVAT SKKNACVSLV FSFLYKVVQ VFSEYFKELE EESIRDNFVI IYELLDELMD FGYPQTTDSK ILQEYITQEG HKLETGAPRP PATVTNAVSW R SEGIKYRK NEVFLDVIEA VNLLVSANGN VLRSEIVGSI KMRVFLSGMP ELRLGLNDKV LFDNTGRGKS KSVELEDVKF HQ CVRLSRF ENDRTISFIP PDGEFELMSY RLNTHVKPLI WIESVIEKHS HSRIEYMVKA KSQFKRRSTA NNVEIHIPVP NDA DSPKFK TTVGSVKWVP ENSEIVWSVK SFPGGKEYLM RAHFGLPSVE AEDKEGKPPI SVKFEIPYFT TSGIQVRYLK IIEK SGYQA LPWVRYITQN GDYQLRTQ

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Macromolecule #6: AP-1 complex subunit sigma-3

MacromoleculeName: AP-1 complex subunit sigma-3 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.321338 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MIHFILLFSR QGKLRLQKWY ITLPDKERKK ITREIVQIIL SRGHRTSSFV DWKELKLVYK RYASLYFCCA IENQDNELLT LEIVHRYVE LLDKYFGNVC ELDIIFNFEK AYFILDEFII GGEIQETSKK IAVKAIEDSD MLQEVSTVCQ TMGER

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Macromolecule #7: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 2 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

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Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.8 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
137.0 mMNaClsodium chloride
2.7 mMKClpotassium chloride
10.0 mMNa2HPO4Sodium phosphate dibasic
1.8 mMKH2PO4Potassium Phosphate, Monobasic

Details: PBS buffer
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab-initio in cryosparc
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.34 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 322238
Initial angle assignmentType: OTHER / Details: Ab-initio in cryosparc
Final angle assignmentType: OTHER / Details: Cryosparc non-uniform reconstruction
FSC plot (resolution estimation)

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